I don't think I'll ever have a PS, but I think I can still make the comparison as I have two AP's and other stock PRSi. The first PRS I ever bought was my 2006 Cu24 AP. Got it new at GC. That guitar continues to be the best sounding PRS I have ever played. So with only that guitar to go by it is simply no contest. AP's have better tone than any stock PRSi. But last year I picked up a 20th Anni AP. It is a 2006 SC and I happen to have one of the old SC's to compare it too. Guess what, the 2000 SC kicks it's butt in tone.
So the answer is, not all guitars are equal, and it doesn't matter if it was a PS, or AP, or stock, if the woods and the hardware and the stars all align, you get one of the great ones. Now I do think that with the best quality woods, and the best build methods, you have a better chance of getting one of those great ones. That is why PRS guitars are more consistent than other companies, but within the PRS family of guitars, you can get a great one out of stock just as you can out of AP or PS offerings.